Huntington's disease (HD) is a devastating fatal neurodegenerative disorder caused by the expansion of a polymorphic CAG repeat in the HD gene that triggers cell death with a specificity towards neurons in the striatum and cortex. Although the underlying genetic mutation was discovered over 15 years ago, there is still no cure or effective treatment despite extensive efforts to understand the molecular pathways that lead to neurodegeneration. In recent years it has become apparent that the HD CAG repeat mutation undergoes dramatic tissue-specific somatic expansion, particularly in the brain regions affected in the disorder. This raises the hypothesis that somatic HD CAG length increases in target tissues contribute to HD pathogenesis. Data that we have generated during the past funding cycle both in accurate genetic Hdh CAG knock-in mouse models of HD and in postmortem brain from HD individuals strongly support this hypothesis, implying that factors that modify somatic instability may also be modifiers of disease. Here we propose experiments to elucidate further a) the factors that contribute to somatic instability and HD pathogenesis, and b) the relationship of somatic instability to disease phenotypes. In Aim 1 we will identify and characterize the genetic variants that underlie the difference in somatic instability and the difference in an early phenotype between congenic Hdh CAG knock-in mouse strains on two inbred genetic backgrounds. In Aim 2 we will cross Hdh CAG knock-in mice onto a mouse background (Msh3-/-) that displays no somatic instability and determine the effect on behavioral phenotypes and late-stage pathology. In Aim 3 we will quantify somatic instability in a large collection of HD postmortem brains and perform a genome-wide association study for modifiers of somatic instability in HD patients. We will also investigate instability in neurons derived from induced pluripotent stem (iPS) cells from HD patients with the aim of generating a cell culture model of instability as an alternative to screen for modifiers of instability in humans. Together, these studies will provide insight into the factors that contribute to somatic instability and the HD pathogenic process. This will lead to novel therapeutic targets both for HD and other trinucleotide repeat diseases based upon a strategy of attacking the DNA mutation itself.